Full-length gene polymorphism of the non-classical HLA-E in Estonian individuals

Estonia is a small country in the Baltic region of Northern Europe with 1.3 million inhabitants. As a coastal area, the population of Estonia was subjected to migration influences. Due to this admixture of populations, HLA gene diversity in Estonia is interesting to study with regard to allele frequencies, haplotypes, and polymorphism. In this study, we focused on HLA-E polymorphism within the Estonian population and compared these with the polymorphism identified in other populations. Full-length HLA-E sequencing of 143 individuals originating from Estonia show dimorphism frequencies at amino acid position 107 (0.55 R vs 0.45 G) comparable to other populations. Within the study population, 16 different HLA-E alleles were identified, including four novel alleles. These 16 alleles encode four different protein variants. Despite a strong differentiation between the South-East and the rest of the Estonian country, no allele frequency differences for HLA-E between these regions were identified. Comparing the allele and SNP frequencies to frequencies found in the different neighboring countries revealed no major differences, except for the SNP encoding for HLA-E*01:06. Association analysis between classical HLA class I genes and polymorphism at amino acid position 107 of HLA-E revealed higher frequencies of HLA-A*01 with R107 and HLA-A*03 and HLA-C*04 with G107. In summary, our study provides new insights into HLA-E variation within the Estonian population and demonstrates that its level of polymorphism is comparable to those observed in other global populations.